Methicillin-resistant Staphylococcus aureus (MRSA) are a leading cause of infectious disease in the United States and elsewhere in the world; these bacteria have acquired resistance to all relevant classes of antibiotics and have become established in community and healthcare environments. Staphylococcus epidermidis and other coagulase-negative staphylococci, once exclusively considered to be commensal species, have emerged as a leading cause of infections associated with indwelling medical devices. Much of the human morbidity and mortality caused by staphylococci are due to a small number of successful, widespread clones. In the current proposal, we seek to exploit the power of rapid next-generation sequencing to obtain a more complete perspective of clone emergence and adaptation for several pathogenic staphylococci. Specifically, we will (1) elucidate fine-scale population structure and the origins, patterns of geographic spread, and evolution of clinically important traits of the USA300 MRSA clone, to characterize an ongoing epidemic, identify biomarkers of key variants, and provide baseline data for future epidemiological interventions; (2) validate coarse-scale population structure within pathogenic coagulase-negative species to identify novel biomarkers of pathogenic variants; (3) compare genome-wide targets of long-term positive selection in S. aureus and S. epidermidis and reveal the importance of balanced polymorphisms to specific antimicrobial resistances.